BitTorrent
For bittorrent it is probably not so helpful to torrify data. Compared to the amount of damage you will do to your throughput and the amount of damage you will do to the Tor network, torryfing data is overkill for the protection you gain. Aside from search index logs and tracker http logs, the attacks needed to determine who is downloading a torrent are somewhat similar to attacks on Tor: the adversary has to be running torrent clients and watching to see who connects to them. This is hard to do on a large scale. You are probably much more at risk for showing up in the webserver logs for popular trackers and index sites.
For this reason, you may want to use tor to communicate with the tracker. For this, just add --tracker-proxy 127.0.0.1:8118:
btlaunchmanycurses --tracker_proxy 127.0.0.1:8118 <directory>
Whilst the above may work to some extent, anonymising the client to the tracker means other clients are unable to download from the Torified client. This leaves it functioning as a Leech which severely degrades its performance within the swarm. This issue applies to the Bittorrent protocol in general, regardless of the client software employed.
µTorrent
Again, torifying the bittorrent traffic of µTorrent would just add more overhead and reduce your transfer throughput a lot. It also severely taxes the Tor network and is considered poor etiquette. The following image shows how to configure µTorrent to torify tracker traffic. Note the unchecked Use proxy server for peer-to-peer connections. Checking this will severely limit transfer speeds and needlesly tax the Tor network.
Azureus
Again, pretty much all you really need to do here is to proxy tracker communications. There is an option for this under the connections pane in Azureus. Fill in 127.0.0.1 9050 for the SOCKS proxy for tracker data.
For more information on setting up torrents tracked via hidden service (which is not really taxing), and to be thoroughly confused by other possibilites, see: http://azureus.sourceforge.net/doc/AnonBT/. Super Seeding is another option if you are the first to seed a file and want to optimally distribute it anonymously. This is an acceptable exception to the request not to torify data.
rTorrent
rTorrent can use a proxy for communicating over HTTP. One merely has to edit ~/.rtorrent.rc and insert something like the following:
http_proxy = http://127.0.0.1:8118/